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- PDB-3f80: (S)-2-amino-6-nitrohexanoic acid binds to human arginase I throug... -

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Basic information

Entry
Database: PDB / ID: 3f80
Title(S)-2-amino-6-nitrohexanoic acid binds to human arginase I through multiple nitro-metal coordination interactions in the binuclear manganese cluster. Resolution 1.60 A.
ComponentsArginase-1
KeywordsHYDROLASE / Nitronium group coordination / surface plasmon resonance / Alternative splicing / Arginine metabolism / Cytoplasm / Disease mutation / Manganese / Metal-binding / Phosphoprotein / Polymorphism / Urea cycle
Function / homology
Function and homology information


positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / : / urea cycle / response to nematode / defense response to protozoan / negative regulation of type II interferon-mediated signaling pathway ...positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / : / urea cycle / response to nematode / defense response to protozoan / negative regulation of type II interferon-mediated signaling pathway / negative regulation of activated T cell proliferation / L-arginine catabolic process / negative regulation of T cell proliferation / specific granule lumen / azurophil granule lumen / manganese ion binding / adaptive immune response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleus / cytoplasm / cytosol
Similarity search - Function
Arginase / Ureohydrolase domain / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-nitro-L-norleucine / : / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDi Costanzo, L. / Christianson, D.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: (S)-2-Amino-6-nitrohexanoic Acid Binds to Human Arginase I through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster.
Authors: Zakharian, T.Y. / Di Costanzo, L. / Christianson, D.W.
History
DepositionNov 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginase-1
B: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1328
Polymers69,5602
Non-polymers5726
Water7,098394
1
A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,72615
Polymers104,3403
Non-polymers1,38712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5620 Å2
ΔGint-18 kcal/mol
Surface area33080 Å2
MethodPISA
2
B: Arginase-1
hetero molecules

B: Arginase-1
hetero molecules

B: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6699
Polymers104,3403
Non-polymers3306
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6110 Å2
ΔGint-44 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.337, 90.337, 69.329
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Arginase-1 / Type I arginase / Liver-type arginase


Mass: 34779.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05089, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-6HN / 6-nitro-L-norleucine


Type: L-peptide linking / Mass: 176.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.61 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.468
ReflectionResolution: 1.6→50 Å / Num. all: 83380 / Num. obs: 83380 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.5 / Num. unique all: 8330 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS0.9refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZAV, mon. A

2zav


Resolution: 1.6→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.184 3981 RANDOM
Rwork0.147 --
all-80874 -
obs-80874 -
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4762 0 28 394 5184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.4
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONC_improper_angle_degree0.9
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.213

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